•Ca-deficient HA and carbonate CHA apatites were obtained under US or MW radiation.•The influence of US or MW radiation significantly shortens HA formation.•The cooling of reaction system has led to the formation of pure HA.•US and MW influences increase the bioactivity of apatites.•Thermal stability of apatites, synthesized under US and MW radiations, decreases. The samples of hydroxyapatite and carbonate substituted hydroxyapatite (CHA) were obtained under the influence of physical factors, namely ultrasound (US) and microwave (MW) radiations. The results of Fourier transform infrared spectroscopy and X-ray diffraction analysis have proved the formation of the calcium deficient hydroxyapatite and B-type CHA with the Ca/P ratio in the ranges 1.62–1.87. In vitro studies have showed the increased bioactivity of the samples, synthesized under the influence of physical factors as compared to the standard ones. The samples of both groups, synthesized under the influence of 600 W MW, have shown the greatest stability in biological environment. In vivo tests confirm that obtained under US and MW radiations hydroxyapatite-based biomaterials are biocompatible, non-toxic and exhibit osteoconductive properties. The usage of US and MW radiations can significantly shorten the time (up to 5–20 min) of obtaining of calcium deficient hydroxyapatite and B-type CHA in nanopowder form, close in structure and composition to the biological hydroxyapatite.